123 lines
4.1 KiB
Bash
123 lines
4.1 KiB
Bash
: ${SHOW_SETTINGS:=false}
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#############################################################################
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# Global settings
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: ${MASTER_IP:=$(wget http://ipinfo.io/ip -qO -)}
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: ${MIP_PRIVATE_NETWORK:="mip_local"}
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: ${COMPOSE_PROJECT_NAME:="mip"}
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: ${PORTAINER_IMAGE:="portainer/portainer"}
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: ${PORTAINER_VERSION:=":latest"}
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: ${PORTAINER_PORT:="9000"}
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: ${PORTAINER_DATA:="${PWD}/portainer"}
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#############################################################################
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# DATABASES
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# Service Parameters
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: ${DB_IMAGE:="hbpmip/postgresraw"}
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: ${DB_VERSION:=":v1.4"}
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# If you want to expose the DB, you have to adapt the values below, as well
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# as uncomment the port section in the docker-compose.yml file.
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: ${DB_HOST:="db"} # Internal hostname, if NOT exposed, defined in docker-compose.yml
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: ${DB_PORT:="5432"} # Internal port, if NOT exposed, default PostgreSQL port
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: ${DB_DATA:="${PWD}/postgres"}
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: ${DB_DATASETS:="${PWD}/datasets"}
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: ${DB_USER_ADMIN:="postgres"}
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: ${DB_PASSWORD_ADMIN:="test"}
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# Databases Definitions:
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# 1. To add a new DB, copy the last 3 lines below and increment the id
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# 2. Add the new number in DB_CREATE_LIST
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: ${DB_NAME1:="meta"}
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: ${DB_USER1:="meta"}
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: ${DB_PASSWORD1:="metapwd"}
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: ${DB_NAME2:="features"}
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: ${DB_USER2:="features"}
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: ${DB_PASSWORD2:="featurespwd"}
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: ${DB_NAME3:="woken"}
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: ${DB_USER3:="woken"}
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: ${DB_PASSWORD3:="wokenpwd"}
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: ${DB_NAME4:="portal"}
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: ${DB_USER4:="portal"}
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: ${DB_PASSWORD4:="portalpwd"}
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# Database setup tools
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: ${DB_CREATE_IMAGE:="hbpmip/create-databases"}
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: ${DB_CREATE_VERSION:=":1.0.0"}
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# List of databases to create
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: ${DB_CREATE_LIST:="1 2 3 4"}
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#: ${METADATA_SETUP_IMAGE:="hbpmip/sample-meta-db-setup"}
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#: ${METADATA_SETUP_VERSION:=":0.4.0"}
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: ${METADATA_SETUP_IMAGE:="hbpmip/mip-cde-meta-db-setup"} # Stable Config
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: ${METADATA_SETUP_VERSION:=":1.1.1"} # Stable Config
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: ${METADATA_SETUP_DB:=${DB_NAME1}}
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: ${SAMPLE_SETUP_IMAGE:="hbpmip/sample-data-db-setup"}
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#: ${SAMPLE_SETUP_VERSION:=":0.5.0"}
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: ${SAMPLE_SETUP_VERSION:=":0.3.2"} # Stable Config
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: ${SAMPLE_SETUP_DB:=${DB_NAME2}}
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: ${ADNI_MERGE_SETUP_IMAGE:="registry.gitlab.com/hbpmip_private/adni-merge-db-setup"}
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: ${ADNI_MERGE_SETUP_VERSION:=":1.4.2"}
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: ${ADNI_MERGE_SETUP_DB:=${DB_NAME2}}
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: ${EDSD_SETUP_IMAGE:="registry.gitlab.com/hbpmip_private/edsd-data-db-setup"}
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: ${EDSD_SETUP_VERSION:=":1.3.2"}
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: ${EDSD_SETUP_DB:=${DB_NAME2}}
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: ${PPMI_SETUP_IMAGE:="registry.gitlab.com/hbpmip_private/ppmi-data-db-setup"}
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: ${PPMI_SETUP_VERSION:=":1.0.2"}
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: ${PPMI_SETUP_DB:=${DB_NAME2}}
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: ${WOKEN_SETUP_IMAGE:="hbpmip/woken-db-setup"}
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: ${WOKEN_SETUP_VERSION:=":1.0.2"}
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: ${WOKEN_SETUP_DB:=${DB_NAME3}}
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# List of databases to populate
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#: ${DB_SETUP_LIST:="SAMPLE_SETUP"}
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: ${DB_SETUP_LIST:="ADNI_MERGE_SETUP EDSD_SETUP PPMI_SETUP"} # Stable Config
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#############################################################################
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# Federation Services
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: ${CONSUL_IMAGE:="progrium/consul"}
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: ${CONSUL_VERSION:="latest"}
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: ${EXAREME_IMAGE:="hbpmip/exareme"}
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: ${EXAREME_VERSION:="v5"}
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: ${EXAREME_UI:="${PWD}/exareme-ui"}
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: ${EXAREME_ROLE:=""} # The default value is set to the federation node role (worker or manager)
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: ${EXAREME_KEYSTORE_PORT:="8500"}
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: ${EXAREME_KEYSTORE:="exareme-keystore:${EXAREME_KEYSTORE_PORT}"}
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: ${EXAREME_MODE:="global"}
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: ${EXAREME_WORKERS_WAIT:="0"} # Wait for N workers
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: ${EXAREME_LDSM_ENDPOINT:="query"}
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: ${EXAREME_LDSM_RESULTS:="all"}
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: ${EXAREME_LDSM_DATAKEY:="output"} # query used with output, query-start with data
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# Exareme LDSM Settings
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: ${LDSM_USERNAME:=${DB_USER2}}
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: ${LDSM_PASSWORD:=${DB_PASSWORD2}}
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: ${LDSM_HOST:=""} # The default value is set to the federation node
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: ${LDSM_PORT:=${DB_PORT}}
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: ${LDSM_DB:=${DB_NAME2}}
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: ${FEDERATION_NODE:=""} # Invalid default value, this a required argument of start.sh
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#############################################################################
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# Local Services
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#: ${FEATURES_LOCAL_TABLE:="cde_features_a"}
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: ${FEATURES_LOCAL_TABLE:="mip_cde_features"} # Stable Config
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: ${DB_UI_IMAGE:="hbpmip/postgresraw-ui"}
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: ${DB_UI_VERSION:=":v1.5"}
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: ${DB_UI_PORT:="31555"} # External port, if exposed
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: ${DB_UI_FEDERATION_SOURCES:="harmonized_clinical_data"}
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: ${DB_UI_LOCAL_SOURCES:="mip_cde_features harmonized_clinical_data"}
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